How Can I Instance an Animated Cycles Gradient Material?
Try the setVertexColor Node.

It seems not so intuitive at first, but it's the per object iterator way to assign the color to instanced geometry. You need to set the value to 'Col' and then back in the Material Node editor use the Attribute node and put 'Col' (for Name field) or what-have-you there too.

Hope I understood your problem. Seems I ended up here so maybe others will find that useful.

I was actually looking for a color ramp node in animation nodes, but I suppose you could take a different single value in this way and pass it through a ramp too.